Danny, that really depends on how extensive is the root rot. if it is only superficial and the remaining roots are uninfected, removing the sphag and the infected foots, sprinkle with some cinnamon powder/dust with antifungal and do the bark replacement (but i prefer leave it empty for 2-3 days for the infected area to dry up before covering it). however oncidium are quite hardy as i know, as long as the infection is superficial, it should not affect the spike development.
you took any pic during the process? perhaps with some pics other forum member can help you better and also what media is the plant potted with?
best of luck and hopefully to see your post with the bloom soon